Merge pull request #728 from kevin218/kbs

Stage 4cal (Calibrated Stellar Spectra)

demos/JWST/CalibratedStellarSpectra/S2_nircam_wfss_template.ecf

@@ -0,0 +1,23 @@
+# Eureka! Control File for Stage 2: Data Reduction
+
+# Stage 2 Documentation: https://eurekadocs.readthedocs.io/en/latest/ecf.html#stage-2
+
+suffix                  rateints     # Data file suffix
+
+# Controls the cross-dispersion extraction
+tsgrism_extract_height  None    # Use None to rely on the default parameters
+
+# Note: different instruments and modes will use different steps by default
+skip_flat_field         False
+skip_photom             False	# Recommended to skip to get better uncertainties out of Stage 3. Set this to False if you want to compute calibrated stellar spectra.
+skip_extract_1d         True
+
+# Diagnostics
+hide_plots              True    # If True, plots will automatically be closed rather than popping up
+
+# Project directory
+topdir                  /home/User/Data/JWST-Sim/NIRCam/
+
+# Directories relative to topdir
+inputdir                Stage1
+outputdir               Stage2

demos/JWST/CalibratedStellarSpectra/S2_nirspec_fs_template.ecf

@@ -0,0 +1,21 @@
+# Eureka! Control File for Stage 2: Data Reduction
+
+# Stage 2 Documentation: https://eurekadocs.readthedocs.io/en/latest/ecf.html#stage-2
+
+suffix                  rateints    # Data file suffix
+
+# Note: different instruments and modes will use different steps by default
+skip_wavecorr           True    # By default is skipped for TSO data
+skip_flat_field         False   # Set this to False if you want to compute calibrated stellar spectra.
+skip_photom             False   # Recommended to skip to get better uncertainties out of Stage 3. Set this to False if you want to compute calibrated stellar spectra.
+skip_extract_1d         True
+
+# Diagnostics
+hide_plots              True    # If True, plots will automatically be closed rather than popping up
+
+# Project directory
+topdir                  /home/User/Data/JWST-Sim/NIRSpec/
+
+# Directories relative to topdir
+inputdir                Stage1
+outputdir               Stage2

demos/JWST/CalibratedStellarSpectra/S3_nircam_wfss_template.ecf

@@ -0,0 +1,66 @@
+# Eureka! Control File for Stage 3: Data Reduction
+
+# Stage 3 Documentation: https://eurekadocs.readthedocs.io/en/latest/ecf.html#stage-3
+
+ncpu            4           # Number of CPUs
+nfiles          1           # The number of data files to analyze simultaneously
+max_memory      0.5         # The maximum fraction of memory you want utilized by read-in frames (this will reduce nfiles if need be)
+indep_batches   False       # Independently treat each batch of files? Strongly recommended to leave this as False unless you have a clear reason to set it to True.
+suffix          calints     # Data file suffix
+
+calibrated_spectra  True   # Set True to generate flux-calibrated spectra/photometry in mJy
+                            # Set False to convert to electrons
+
+# Subarray region of interest
+ywindow         [5,64]      # Vertical axis as seen in DS9
+xwindow         [790, 1950]  # Horizontal axis as seen in DS9
+src_pos_type    gaussian    # Determine source position when not given in header (Options: header, gaussian, weighted, max, hst, or a numeric value)
+record_ypos     False        # Option to record the y position and width for each integration (only records if src_pos_type is gaussian)
+poly_wavelength	True		# Use an updated polynomial wavelength solution for NIRCam longwave spectroscopy instead of the linear wavelength solution currently assumed by STScI
+dqmask          True        # Mask pixels with an odd entry in the DQ array
+expand          1           # Super-sampling factor along cross-dispersion direction
+
+# Outlier rejection along time axis
+ff_outlier      False       # Set False to use only background region (recommended for deep transits)
+                            # Set True to use full frame (works well for shallow transits/eclipses)
+bg_thresh       [4,4]       # Double-iteration X-sigma threshold for outlier rejection along time axis
+
+# Background parameters
+bg_hw           20           # Half-width of exclusion region for BG subtraction (relative to source position)
+bg_deg          0           # Polynomial order for column-by-column background subtraction, -1 for median of entire frame
+bg_method       median        # Options: std (Standard Deviation), median (Median Absolute Deviation), mean (Mean Absolute Deviation)
+p3thresh        5           # X-sigma threshold for outlier rejection during background subtraction
+bg_row_by_row   False       # Row-by-row BG subtraction (only useful for NIRCam)
+bg_x1           None        # Left edge of exclusion region for row-by-row BG subtraction
+bg_x2           None        # Right edge of exclusion region for row-by-row BG subtraction
+
+# Spectral extraction parameters
+spec_hw         12           # Half-width of aperture region for spectral extraction (relative to source position)
+fittype         meddata     # Method for constructing spatial profile (Options: smooth, meddata, poly, gauss, wavelet, or wavelet2D)
+median_thresh   10          # Sigma threshold when flagging outliers in median frame, when fittype=meddata and window_len > 1
+window_len      7           # Smoothing window length, for median frame or when fittype = smooth or meddata (when computing median frame). Can set to 1 for no smoothing when computing median frame for fittype=meddata.
+prof_deg        3           # Polynomial degree, when fittype = poly
+p5thresh        10          # X-sigma threshold for outlier rejection while constructing spatial profile
+p7thresh        7           # X-sigma threshold for outlier rejection during optimal spectral extraction
+
+# Curvature treatment
+curvature       correct     # How to manage the curved trace on the detector (Options: None, correct)
+
+# Diagnostics
+isplots_S3      3           # Generate few (1), some (3), or many (5) figures (Options: 1 - 5)
+nplots          5           # How many of each type of figure do you want to make per file?
+vmin            0.97        # Sets the vmin of the color bar for Figure 3101.
+vmax            1.03        # Sets the vmax of the color bar for Figure 3101.
+time_axis       'y'         # Determines whether the time axis in Figure 3101 is along the y-axis ('y') or the x-axis ('x')
+testing_S3      False       # Boolean, set True to only use last file and generate select figures
+hide_plots      True        # If True, plots will automatically be closed rather than popping up
+save_output     True        # Save outputs for use in S4
+save_fluxdata   False       # Save the much larger FluxData.h5 outputs which can be useful for debugging or comparisons between different pipelines
+verbose         True        # If True, more details will be printed about steps
+
+# Project directory
+topdir          /home/User/Data/JWST-Sim/NIRCam/
+
+# Directories relative to topdir
+inputdir        Stage2      # The folder containing the outputs from Eureka!'s S2 or JWST's S2 pipeline (will be overwritten if calling S2 and S3 sequentially)
+outputdir       Stage3

demos/JWST/CalibratedStellarSpectra/S3_nirspec_fs_template.ecf

@@ -0,0 +1,63 @@
+# Eureka! Control File for Stage 3: Data Reduction
+
+# Stage 3 Documentation: https://eurekadocs.readthedocs.io/en/latest/ecf.html#stage-3
+
+ncpu            4           # Number of CPUs
+nfiles          1           # The number of data files to analyze simultaneously
+max_memory      0.5         # The maximum fraction of memory you want utilized by read-in frames (this will reduce nfiles if need be)
+indep_batches   False       # Independently treat each batch of files? Strongly recommended to leave this as False unless you have a clear reason to set it to True.
+suffix          calints     # Data file suffix
+
+calibrated_spectra  True    # Set True to generate flux-calibrated spectra/photometry in mJy
+                            # Set False to convert to electrons
+
+# Subarray region of interest
+ywindow         [2,28]      # Vertical axis as seen in DS9
+xwindow         [804,2042]  # NRS1, Horizontal axis as seen in DS9
+# xwindow         [5,2028]    # NRS2, Horizontal axis as seen in DS9
+src_pos_type    gaussian    # Determine source position when not given in header (Options: header, gaussian, weighted, max, hst, or a numeric value)
+record_ypos     False       # Option to record the y position and width for each integration (only records if src_pos_type is gaussian)
+dqmask          False       # Mask pixels with an odd entry in the DQ array
+expand          1           # Super-sampling factor along cross-dispersion direction
+
+# Outlier rejection along time axis
+ff_outlier      False       # Set False to use only background region (recommended for deep transits)
+                            # Set True to use full frame (works well for shallow transits/eclipses)
+bg_thresh       [6,6]       # Double-iteration X-sigma threshold for outlier rejection along time axis
+
+# Background parameters
+bg_hw           9           # Half-width of exclusion region for BG subtraction (relative to source position)
+bg_deg          None        # Polynomial order for column-by-column background subtraction, -1 for median of entire frame
+bg_method       median      # Options: std (Standard Deviation), median (Median Absolute Deviation), mean (Mean Absolute Deviation)
+p3thresh        10          # X-sigma threshold for outlier rejection during background subtraction
+
+# Spectral extraction parameters
+spec_hw         6           # Half-width of aperture region for spectral extraction (relative to source position)
+fittype         meddata     # Method for constructing spatial profile (Options: smooth, meddata, poly, gauss, wavelet, or wavelet2D)
+median_thresh   5           # Sigma threshold when flagging outliers in median frame, when fittype=meddata and window_len > 1
+window_len      13          # Smoothing window length, for median frame or when fittype = smooth or meddata (when computing median frame). Can set to 1 for no smoothing when computing median frame for fittype=meddata.
+prof_deg        3           # Polynomial degree, when fittype = poly
+p5thresh        10          # X-sigma threshold for outlier rejection while constructing spatial profile
+p7thresh        10          # X-sigma threshold for outlier rejection during optimal spectral extraction
+
+# Curvature treatment
+curvature       correct     # How to manage the curved trace on the detector (Options: None, correct)
+
+# Diagnostics
+isplots_S3      3           # Generate few (1), some (3), or many (5) figures (Options: 1 - 5)
+nplots          1           # How many of each type of figure do you want to make per file?
+vmin            0.97        # Sets the vmin of the color bar for Figure 3101.
+vmax            1.03        # Sets the vmax of the color bar for Figure 3101.
+time_axis       'y'         # Determines whether the time axis in Figure 3101 is along the y-axis ('y') or the x-axis ('x')
+testing_S3      False       # Boolean, set True to only use last file and generate select figures
+hide_plots      True        # If True, plots will automatically be closed rather than popping up
+save_output     True        # Save outputs for use in S4
+save_fluxdata   False       # Save the much larger FluxData.h5 outputs which can be useful for debugging or comparisons between different pipelines
+verbose         True        # If True, more details will be printed about steps
+
+# Project directory
+topdir          /home/User/Data/JWST-Sim/NIRSpec/
+
+# Directories relative to topdir
+inputdir        Stage2      # The folder containing the outputs from Eureka!'s S2 or JWST's S2 pipeline (will be overwritten if calling S2 and S3 sequentially)
+outputdir       Stage3

demos/JWST/CalibratedStellarSpectra/S4cal_template.ecf

@@ -0,0 +1,36 @@
+# Eureka! Control File for Stage 4cal: Calibrated Stellar Spectra
+
+# Stage 4cal Documentation: https://eurekadocs.readthedocs.io/en/latest/ecf.html#stage-4cal
+
+# Transit/Eclipse time
+t0              110.810782      # BJD
+time_offset     60000           # Optional; time offset
+
+# Orbital parameters
+rprs            0.07194         # Planet-star radius ratio
+period          4.2344923       # Orbital period (in Days)
+inc             87.799          # orbital inclination (in degrees)
+ars             12.518          # Semi-major axis to stellar radius ratio
+# Transit durations. When given, the orbital parameters are ignored.
+# t14             None            # Total transit duration, from t1 to t4
+# t23             None            # Full transit duration, from t2 to t3
+
+# Light curve to be used before t1 and after t4 for the baseline flux,
+# which includes flux from (t1 - base_dur) to t1 and t4 to (t4 + base_dur).
+base_dur        0.1             # Days
+
+# Outlier detection
+smoothing       1000            # A good starting point is the number of datapoints (i.e. wavelengths).  A value of 0 will apply interpolation.
+sigma_thresh    [4,4,4]         # Three rounds of 4-sigma clipping ([4,4,4])
+
+# Diagnostics
+isplots_S4cal   3               # Generate few (1), some (3), or many (5) figures (Options: 1 - 5)
+nbin_plot       200             # The number of time bins that should be used for figure 4202
+hide_plots      False           # If True, plots will automatically be closed rather than popping up
+
+# Project directory
+topdir          /home/User/Data/JWST-Sim/NIRSpec/
+
+# Directories relative to topdir
+inputdir        Stage3          # The folder containing the calibrated stellar spectra from Eureka!'s S3 pipeline
+outputdir       Stage4cal

demos/JWST/CalibratedStellarSpectra/run_eureka.py

@@ -0,0 +1,28 @@
+import os
+import eureka.lib.plots
+import eureka.S1_detector_processing.s1_process as s1
+import eureka.S2_calibrations.s2_calibrate as s2
+import eureka.S3_data_reduction.s3_reduce as s3
+import eureka.S4cal_StellarSpectra.s4cal_StellarSpec as s4cal
+
+# Set up some parameters to make plots look nicer.
+# You can set usetex=True if you have LaTeX installed
+eureka.lib.plots.set_rc(style='eureka', usetex=False, filetype='.png')
+
+# eventlabel = 'imaging_template'
+# eventlabel = 'miri_lrs_template'
+eventlabel = 'nirspec_fs_template'
+# eventlabel = 'nircam_wfss_template'
+ecf_path = '.'+os.sep
+
+if __name__ == '__main__':
+    # To skip one or more stages that were already run,
+    # just comment them out below
+
+    meta = s1.rampfitJWST(eventlabel, ecf_path=ecf_path)
+
+    meta = s2.calibrateJWST(eventlabel, ecf_path=ecf_path)
+
+    spec, meta = s3.reduce(eventlabel, ecf_path=ecf_path)
+
+    meta, spec, ds = s4cal.medianCalSpec(eventlabel, ecf_path=ecf_path)

docs/media/S4cal_template.ecf

@@ -0,0 +1,36 @@
+# Eureka! Control File for Stage 4cal: Calibrated Stellar Spectra
+
+# Stage 4cal Documentation: https://eurekadocs.readthedocs.io/en/latest/ecf.html#stage-4cal
+
+# Transit/Eclipse time
+t0              110.810782      # BJD
+time_offset     60000           # Optional; time offset
+
+# Orbital parameters
+rprs            0.07194         # Planet-star radius ratio
+period          4.2344923       # Orbital period (in Days)
+inc             87.799          # orbital inclination (in degrees)
+ars             12.518          # Semi-major axis to stellar radius ratio
+# Transit durations. When given, the orbital parameters are ignored.
+# t14             None            # Total transit duration, from t1 to t4
+# t23             None            # Full transit duration, from t2 to t3
+
+# Light curve to be used before t1 and after t4 for the baseline flux,
+# which includes flux from (t1 - base_dur) to t1 and t4 to (t4 + base_dur).
+base_dur        0.1             # Days
+
+# Outlier detection
+smoothing       1000            # A good starting point is the number of datapoints (i.e. wavelengths).  A value of 0 will apply interpolation.
+sigma_thresh    [4,4,4]         # Three rounds of 4-sigma clipping ([4,4,4])
+
+# Diagnostics
+isplots_S4cal   3               # Generate few (1), some (3), or many (5) figures (Options: 1 - 5)
+nbin_plot       200             # The number of time bins that should be used for figure 4202
+hide_plots      False           # If True, plots will automatically be closed rather than popping up
+
+# Project directory
+topdir          /home/User/Data/JWST-Sim/NIRSpec/
+
+# Directories relative to topdir
+inputdir        Stage3          # The folder containing the calibrated stellar spectra from Eureka!'s S3 pipeline
+outputdir       Stage4cal

docs/source/copyright.rst

@@ -19,4 +19,4 @@ The current main developers of Eureka! are (ordered alphabetically by first name
 - Taylor Bell
 - Yoni Brande
 
-We would also like to acknowledge the valuable `contributions from numerous users<https://github.com/kevin218/Eureka/graphs/contributors>`_ that have helped make Eureka! a success. Thank you!
+We would also like to acknowledge the valuable `contributions from numerous users <https://github.com/kevin218/Eureka/graphs/contributors>`_ that have helped make Eureka! a success. Thank you!